Towards exhaustive community ecology via DNA metabarcoding

Abstract

Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and to evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability to perform biodiversity inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority of metabarcoding studies published in the last years used just one or two markers and analysed a limited number of taxonomic groups. Here, we provide an overview of emerging approaches that can allow all‐taxa biological inventories. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers, shotgun sequencing and capture enrichment may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. Here, we identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future. More holistic reconstructions of ecological communities can greatly increase the value of metabarcoding studies, improving understanding of the consequences of ongoing environmental changes on the multiple components of biodiversity.

Metabarcoding the eukaryotic community of a threatened, iconic Mediterranean habitat: Posidonia oceanica seagrass meadows

“…Taxonomically broad analyses of communities via metabarcoding can be based on several techniques, each with advantages and shortcomings. The use of universal primers is one of them, but other alternatives are the combination of markers, the use of primer cocktails, or PCR-free approaches (Ficetola and Taberlet, 2023). We chose to use the COI marker and a primer set that has been shown to amplify most eukaryote groups (Wangensteen et al, 2018;Antich et al, 2023).…”

An automated workflow to assess completeness and curate GenBank for environmental DNA metabarcoding: The marine fish assemblage as case study

“…Similarly, biological phenomena such as inter-specific introgression could make sequences from the same species appear more distant than expected and species from different species closer than expected (Viñas & Tudela, 2009). These challenging cases are not limited to the accuracy of the reference database but to the chosen barcode region, and different primer combinations are a promising solution to tackle them (Ficetola & Taberlet, 2023).…”

Insights into Ecological & Evolutionary Processes via community metabarcoding

“…Metabarcoding provides an ideal opportunity to examine questions relating to interaction networks and can provide quantitative assessment of resilience to perturbation. Highlighting the promise and importance of metabarcoding for a holistic understanding of entire interacting assemblages of different trophic groups, Ficetola and Taberlet (2023) review approaches that can reveal biodiversity response to global change. Metabarcoding approaches provide information not only on species occurrences, but also on species interactions, with new approaches using species traits, phylogenetic information, and machine learning algorithms to infer multitrophic and multitaxa interactions.…”